Natural Product: NPC95265

Natural Product IDNPC95265
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
PNZVRNRYBVTQAP-OCRATEHUSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1829520
PubChem CID 56589618
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0002995] Pentacarboxylic acids and derivatives

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey PNZVRNRYBVTQAP-OCRATEHUSA-N
Standard InCHI InChI=1S/C35H40O12/c1-20(36)42-19-34-27(45-30(39)23-13-9-7-10-14-23)17-25-28(46-31(40)24-15-11-8-12-16-24)35(34,47-32(25,4)5)33(6,41)18-26(43-21(2)37)29(34)44-22(3)38/h7-16,25-29,41H,17-19H2,1-6H3/t25-,26+,27+,28-,29+,33+,34-,35+/m1/s1
SMILES CC(=O)OC[C@@]12[C@@H](OC(=O)c3ccccc3)C[C@@H]3[C@H]([C@]2(OC3(C)C)[C@@](C[C@@H]([C@@H]1OC(=O)C)OC(=O)C)(C)O)OC(=O)c1ccccc1

  Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO26437 Maytenus jelskii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[20146433]
NPO26437 Maytenus jelskii Species Celastraceae Eukaryota fruits n.a. n.a. PMID[21856049]
NPO26437 Maytenus jelskii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[27541714]
NPO26437 Maytenus jelskii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26437 Maytenus jelskii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
UNPD: Universal Natural Products Database [PMID: 23638153].
StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
MetaboLights: a metabolomics database [PMID: 27010336].
FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



  NP Quantity Composition/Concentration

Organism ID Organism Name Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



 Biological Activity

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT668 Individual protein P-glycoprotein 1 Homo sapiens Inhibition = 70.0 % PMID[19128055]
NPT668 Individual protein P-glycoprotein 1 Homo sapiens Ki = 390.0 nM DrugMatrix in vivo data: Hematology
NPT668 Individual protein P-glycoprotein 1 Homo sapiens Imax > 90.0 % PMID[21856049]
NPT668 Individual protein P-glycoprotein 1 Homo sapiens Ratio IC50 = 12.73 n.a. PMID[17850214]
NPT668 Individual protein P-glycoprotein 1 Homo sapiens Ratio IC50 = 19.8 n.a. PMID[26034885]
NPT668 Individual protein P-glycoprotein 1 Homo sapiens Ratio IC50 = 21.24 n.a. PMID[11277768]
NPT668 Individual protein P-glycoprotein 1 Homo sapiens Ratio IC50 = 28.6 n.a. PMID[18640035]
NPT668 Individual protein P-glycoprotein 1 Homo sapiens Ratio IC50 = 52.56 n.a. PMID[25211032]
NPT668 Individual protein P-glycoprotein 1 Homo sapiens Ratio IC50 = 165.1 n.a. PMID[16872140]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT886 Cell line NIH3T3 Mus musculus Activity = 76.7 % PMID[4851320]
NPT886 Cell line NIH3T3 Mus musculus Activity = 77.21 % PMID[4851320]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC95265 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.9385 High Similarity NPC97667
0.8806 High Similarity NPC70716
0.8551 High Similarity NPC479042
0.8472 Intermediate Similarity NPC610134
0.84 Intermediate Similarity NPC294512
0.8052 Intermediate Similarity NPC483868
0.7922 Intermediate Similarity NPC176413
0.7922 Intermediate Similarity NPC483885
0.7361 Intermediate Similarity NPC472570
0.7333 Intermediate Similarity NPC6815
0.726 Intermediate Similarity NPC96903
0.7123 Intermediate Similarity NPC11685
0.7123 Intermediate Similarity NPC16912
0.7083 Intermediate Similarity NPC171207
0.7037 Intermediate Similarity NPC479045
0.6842 Remote Similarity NPC481489
0.6806 Remote Similarity NPC479047
0.6806 Remote Similarity NPC191082
0.6806 Remote Similarity NPC291638
0.6667 Remote Similarity NPC472569
0.6575 Remote Similarity NPC4341
0.6538 Remote Similarity NPC481488
0.6533 Remote Similarity NPC479044
0.6494 Remote Similarity NPC282239
0.6494 Remote Similarity NPC472568
0.6486 Remote Similarity NPC177340
0.6267 Remote Similarity NPC67777
0.6267 Remote Similarity NPC43241
0.6234 Remote Similarity NPC57628
0.622 Remote Similarity NPC479041
0.622 Remote Similarity NPC56953
0.6098 Remote Similarity NPC479048
0.6076 Remote Similarity NPC471102
0.6076 Remote Similarity NPC481490
0.6053 Remote Similarity NPC270590
0.6053 Remote Similarity NPC139067
0.6049 Remote Similarity NPC479049
0.5952 Remote Similarity NPC483870
0.5952 Remote Similarity NPC75600
0.5952 Remote Similarity NPC483884
0.5949 Remote Similarity NPC184747
0.5926 Remote Similarity NPC481487
0.5897 Remote Similarity NPC41481
0.5814 Remote Similarity NPC483869
0.5789 Remote Similarity NPC17877
0.5789 Remote Similarity NPC281717
0.575 Remote Similarity NPC106895
0.5676 Remote Similarity NPC200592
0.5676 Remote Similarity NPC610542
0.5658 Remote Similarity NPC483879
0.5641 Remote Similarity NPC158663
0.5625 Remote Similarity NPC266265
0.5584 Remote Similarity NPC483902
0.5584 Remote Similarity NPC472577
0.557 Remote Similarity NPC471104
0.557 Remote Similarity NPC473673
0.5513 Remote Similarity NPC246480
0.5467 Remote Similarity NPC195647
0.5467 Remote Similarity NPC270498
0.5443 Remote Similarity NPC27377
0.5385 Remote Similarity NPC483886
0.5357 Remote Similarity NPC481486
0.5316 Remote Similarity NPC48017
0.5316 Remote Similarity NPC147880
0.5309 Remote Similarity NPC92293
0.5294 Remote Similarity NPC488917
0.5263 Remote Similarity NPC473081
0.525 Remote Similarity NPC471101
0.5238 Remote Similarity NPC609309
0.5185 Remote Similarity NPC471100
0.5185 Remote Similarity NPC605884
0.5181 Remote Similarity NPC127720
0.5062 Remote Similarity NPC148062
0.506 Remote Similarity NPC479043

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC95265 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
A: chemistry similarity;
B: biological targets similarity;
C: networks similarity;
D: cell-based bioactivity similarity;
E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data